Cue-specific remodeling of the neuronal transcriptome through intron retention programs

We provide a comprehensive map of the subcellular localization of mRNAs in mature neurons and reveal that transcripts stably retaining introns are broadly targeted for nuclear retention. We systematically probed the fate of nuclear transcripts upon neuronal stimulation and found that sub-populations of transcripts are bi-directionally regulated in response to neuronal cues: some are targeted for degradation while others undergo splicing completion to generate fully mature mRNAs which are exported to the cytosol. Overall design: Comparative intron retention profiling analysis of RNA-seq data for mouse primary cortical cells treated with bicuculline or BDNF.